Archivio istituzionale della ricerca - Alma Mater Studiorum Università di Bologna
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A robust Bayesian model to quantify and adjust for study quality and conflict of interest in meta-analyses
Get PDFMeta-analyses are vital for synthesizing evidence in medical research, but conflicts of interest can introduce research bias, undermining the reliability of the synthesized findings. This paper proposes a new robust Bayesian meta-analysis model. The model inflates uncertainty of low-quality studies and incorporates a bias term for studies subject to conflicts of interest. Using a random-effects model and sensitivity analysis with bounded probabilities, the model enables robust adjustments for conflicts of interest in meta-analytic contexts. A case study on antidepressant trials illustrates the potential application of the model
Re: Using Deep Learning To Differentiate Among Histology Renal Tumor Types in Computed Tomography Scans
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Crystallographic, electronic and vibrational properties of 2D silicate monolayers
Get PDFPhyllosilicates are promising materials for optoelectronic applications because of their interesting electronic and magnetic properties that can be modulated by specific ionic substitutions. They can be easily exfoliated down to a single layer, enabling their use in specific 2D applications, such as the creation of van der Waals heterostructures and other materials with tailored physical properties. The present work reports a theoretical investigation of the structural, electronic, Raman and infrared properties of the (001) monolayer of phlogopite [K(Mg, Fe)3Si3AlO10(OH)2, with Mg/Fe ratio ≥ 2] and how they change with different Fe2+/Mg2+ substitutions in the structure. Although other cations could occupy the octahedral sheet positions in phlogopite (and phyllosilicate in general), here the focus is only on Fe2+/Mg2+ substitution. To this aim, density functional theory simulations were performed using the B3LYP functional, including long-range interactions in the physical treatment. The structure of the single layer of phlogopite showed a decrease of the tetrahedral rotation angle near the interlayer cations in comparison with that of the bulk mineral, which led to a tetrahedral sheet with a hexagonal pattern close to ideality, and an electronic band structure with a decreased band gap energy, down to about 3 eV. All results were discussed against the few available experimental and theoretical data in the scientific literature, finding good agreement but also further extending the knowledge of this interesting natural 2D material
Predicatori e predicazione nella Postilla detta di Hugues de Saint-Cher
No full textIl saggio analizza come un testo cardine della prima elaborazione teologica dei frati predicatori attivi a Parigi, la Postilla che circola sotto il nome di Hugues de Saint-Cher, presenta e discute il ruolo centrale della predicazione e dei predicatori da un punto di vista ecclesiologico e sociale, con particolare attenzione all' interpretazione di alcune parabole del Vangelo di Luc
A descriptor-free machine learning framework to improve antigen discovery for bacterial pathogens
Get PDFIdentifying protective antigens (PAs), i.e., targets for bacterial vaccines, is challenging as conducting in-vivo tests at the proteome scale is impractical. Reverse Vaccinology (RV) aids in narrowing down the pool of candidates through computational screening of proteomes. Within RV, one prominent approach is to train Machine Learning (ML) models to classify PAs. These models can be used to predict unseen protein sequences and assist researchers in selecting promising candidates. Traditionally, proteins are fed into these models as vectors of biological and physico-chemical descriptors derived from their residue sequences. However, this method relies on multiple third-party software packages, which may be unreliable, difficult to use, or no longer maintained. Furthermore, selecting descriptors is susceptible to biases. Hence, Protein Sequence Embeddings (PSEs)—high-dimensional vectorial representations of protein sequences obtained from pretrained deep neural networks—have emerged as an alternative to descriptors, offering data-driven feature extraction and a streamlined computational pipeline. We introduce PSEs as a descriptor-free representation of protein sequences for ML in RV. We conducted a thorough comparison of PSE-based and descriptor-based pipelines for PA classification across 10 bacterial species evaluated independently. Our results show that the PSE-based pipeline, which leverages the FAIR ESM-2 protein language model, outperformed the descriptor-based pipeline in 9 out of 10 species, with a mean Area Under the Receiver Operating Characteristics curve (AUROC) of 0.875 versus 0.855. Additionally, it achieved superior performance on the iBPA benchmark (0.86 AUROC vs. 0.82) compared to other methods in the literature. Lastly, we applied the pipeline to rank unseen proteomes based on protective potential to guide candidate selection for pre-clinical testing. Compared to the standard RV practice of ranking candidates according to their biological descriptors, our approach reduces the number of pre-clinical tests needed to identify PAs by up to 83% on average
Linguistica dei corpora e informatica umanistica per la valorizzazione plurilingue del patrimonio culturale: implementazione del progetto UniVOCIttà
No full textLa fruizione del patrimonio culturale da parte di un pubblico internazionale rappresenta un’esigenza sempre più rilevante nella società contemporanea. In tale prospettiva si colloca il progetto UniVOCIttà, sviluppato dall’unità di ricerca LBC-CeSLiC del Dipartimento di Lingue, Letterature e Culture Moderne dell’Università di Bologna. Il progetto si inserisce tra le ricerche nel campo dell’informatica umanistica e propone una metodologia innovativa volta alla valorizzazione plurilingue del patrimonio artistico e culturale di Bologna attraverso la creazione di un corpus comparabile plurilingue annotato, composto da scritti di viaggio di personaggi illustri, dal Rinascimento all’epoca contemporanea.
In collaborazione con specialisti di Web Technologies dell’Università di Bologna, è stato realizzato il prototipo di un’applicazione web mobile destinata al turismo culturale, che consente la consultazione della banca dati plurilingue tramite visualizzazioni sia lineari che dinamiche. Poiché le testimonianze letterarie sono attualmente disponibili solo nella lingua originale, è in corso un’implementazione della app nell’ambito di un progetto di dottorato finalizzato all’integrazione delle traduzioni dei contenuti in lingua italiana e nelle altre lingue del progetto. A tal fine, si prevede di testare un sistema di traduzione automatica neurale (DeepL), e un chatbot generativo di ultima generazione (ChatGPT 4o). Tuttavia, considerati i limiti di questi strumenti di intelligenza artificiale nella traduzione di lessemi e termini relativi alle belle arti, gli output verranno sottoposti a una fase di revisione manuale mediante la consultazione di un sotto-corpus comparabile di scritti di viaggio in lingua italiana, attualmente in fase di realizzazione. L’obiettivo finale è di offrire a utenti provenienti da diversi orizzonti linguistici una risorsa digitale che favorisca l’accesso e la valorizzazione del patrimonio artistico e culturale bolognese in una prospettiva plurilingue
New Perspectives on Digital Representation: The Case of the ‘Santa Casa de Misericórdia’ in São Carlos (Brazil)
Get PDFThis research aims to investigate the Italian architectural heritage in Brazil through the
analysis of the ‘Santa Casa de Misericórdia’ hospital in São Carlos, in the state of São
Paulo. As part of the KNOW.IT national project, the work aims to recover and digitally
enhance Italian heritage abroad from the 19th and 20th centuries. The buildings analysed
were either designed or built by Italian architects who emigrated to South America or
constructed using materials and techniques typical of Italian architecture of those years.
The hospital, designed by the Italian architect Samuele Malfatti in 1891, was chosen for its
historical value and its role in the urban context of the city of São Carlos, which, moreover,
continues to perform its function even today. The study aims to create a digital archive
with 3D models and two-dimensional graphical drawings. The methodology includes historical
analysis, photogrammetric survey, and digital modelling using Agisoft Metashape
and 3DF Zephyr software. A total of 636 images were processed, with the maximum resolution
achieved in the models being 3526 × 2097 pixels. The results highlight the influence
of Italian architecture on late 19th-century São Carlos and promote its virtual accessibility
and wide-ranging knowledge
Sustainable breeding and conservation of an autochthonous cattle breed: managing undesirable alleles and inbreeding in the Reggiana population
No full textThe Reggiana breed, an Italian autochthonous cattle genetic resource mainly reared in the Emilia Romagna region, holds a great cultural and economic importance due to the production of the exclusive mono-breed Protected Designation of Origin (PDO) Parmigiano-Reggiano cheese. Maintaining the integrity of this breed is essential for both economic and cultural reasons. The conservation of its genetic diversity provides a significant source of income for farmers in the Emilia Romagna region. Analysing allele frequencies across the population can identify the presence of potential disadvantageous alleles or alleles that may confer non-breed specific characteristics, carried by few heterozygous animals. Although these alleles exist at low frequencies, their potential impact on herd health, breed identity and economic losses could be substantial if not properly managed. For instance, if allele frequencies increase due to genetic drift or inappropriate breeding choices, homozygous animals may exhibit harmful phenotypes or undesirable traits. In this study, a population of approximately 4,000 Reggiana cattle, covering almost the entire breed and all the active sires, using the GeneSeek GGP Bovine 150k SNP chip to identify and manage undesirable alleles that could represent a risk to the breed's health, productivity, and long-term sustainability. Genotyping data were filtered and analysed using PLINK 1.9 software and ad-hoc Python and R scripts. Haplotypes were estimated with SHAPEIT software and the Ghap R package. The study revealedthe presence of several undesirable alleles in heterozygous carriers, already characterised in other cosmopolitan cattle breeds such as Brown Swiss and Holstein. Potential disadvantageous alleles and haplotypes were identified in a few animals, ranging from a minimum of 3 to a maximum of 143 carriers. These alleles, including BH2, HH1, HH3, and JH1, are associated with reproductive issues such as reduced fertility, stillbirths, and postnatal mortality if found in a homozygous state. Additionally, genomic inbreeding in the breed was monitored using runs of homozygosity. The findings highlight the necessity of implementing targeted breeding strategies, such as limiting pairings between carriers of undesirable alleles to eliminate these alleles and their potential impact on population health, without compromising the breed diversity. Inbreeding should also be controlled by introducing optimum contribution selection. These strategies are crucial for the sustainability of this genetic resource and provide a model for the conservation of small autochthonous livestock breeds.
This study was carried out within the Agritech National Research Center (Spoke 1) and received funding from the European Union Next-GenerationEU under the National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.4, Call D. D.3138 published on 12/16/2021 amended D.D. 3175 on 18/12/2021, CN00000022 – CUP J33C22001150008
Area-wide augmentation of Anagyrus vladimiri and Cryptolaemus montrouzieri enhances biological control of mealybugs in Lambrusco vineyards in Northern Italy
No full textAn area-wide augmentative biological control program against vineyard mealybugs was conducted in a Lambrusco vineyard cultivation area in the Emilia-Romagna region (Northern Italy), releasing the parasitoid Anagyrus vladimiri and the predator Cryptolaemus montrouzieri. A sampling program was established to evaluate the biological control efficacy of these natural enemies, within 16 pilot farms, following the principles of the Integrated Pest Management adopted in the region. The effectiveness of the natural enemies was evaluated by comparing the situation before and after 3 years of releases. Results showed that the dominant mealybug was Pseudococcus comstocki (75 % in 2019 and 86 % in 2022), followed by Planococcus ficus. A significant increase in parasitism rate and predator density was recorded in release farms compared to the control ones, with the parasitism rate reaching a median value of about 80 %. Mealybug infestation patterns, and to some extent the activity of natural enemies, showed some variability among the farms monitored. A positive correlation between A. vladimiri and C. mountrouzieri biocontrol activity revealed a lack of competition between them. The increase of insecticide treatments in release farms did not result in a higher efficacy of control, but negatively affected the parasitism rate. In conclusion, augmentative biological control promoted the activity of natural enemies, likely enhancing the dispersal of parasitoids. Our results highlight the need to combine a biological control strategy with an Integrated Pest Management approach based on the reduction of insecticide sprays, the use of more selective active ingredients, and the proper timing of treatments
GinExtraMed: Focus on Rosa canina L. Extract Encapsulated into Glycethosomes and Allanthosomes for Accelerating Skin Wound Healing
No full textBackground/Objectives: Over the last decade, the development of innovative wound products has continued to be a focus of intense research to meet the huge demand of patients. The aim of this work was to develop novel medicated Spanish broom wound dressings capable of releasing Rosa canina extract, recognized for its high antioxidant activity. Methods: Rosa canina extract was encapsulated in two different nanocarriers, namely glycethosomes and allanthosomes. The physico-chemical and functional characteristics of the obtained vesicles were described, including their size, particle size distribution, zeta potential, and encapsulation efficiency (EE). In addition, vesicles cytotoxicity and cell proliferation were evaluated on human fibroblasts. Furthermore, loaded vesicles were sunk into Spanish broom dressings, analyzed by confocal microscopy, and, finally, evaluated for their wound healing ability by scratch test. Results: Both carriers are nanometric in size, with a good EE (>70%), and a negative zeta potential. Additionally, vesicles are biosafe, non-cytotoxic, and lead to complete closure of the scratch in about 30 h. Conclusions: The findings showed that the developed Spanish broom dressings have the potential to be an efficient and innovative wound care product for accelerating skin wounds